Jan. 27th 2015

  • Goal : To identify baseline DNA methylation markers that predict the change in PHQ (Aim 1)

  • Model : PHQchange = a + b * BaselineMethylation + e

  • Sites : 483806

  • Sample size: 65

  • Multiple Testing Correction : Bonferroni

  • 5% MinP Cutoff - Raw PHQchange : 1.46e-08

  • 5% MinP Cutoff - INV PHQchange : 2.92e-07

Association Test

Raw PHQchange ~ Baseline Methylation

QQplot of pvals based on Raw PHQchange and CI

Results based on Raw PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg25660390 17 NA 73073700 0.003 0e+00 0.0043 65
cg22577606 7 CYP51A1 91763103 0.010 1e-07 0.0267 65
cg07219643 12 WSB2 118499016 0.001 1e-07 0.0362 65
cg15286044 10 CRTAC1 99789971 0.004 1e-07 0.0422 65
cg23932859 5 MEGF10 126625777 0.008 2e-07 0.1094 65
cg23679073 2 ZC3H15 187350909 0.002 3e-07 0.1558 65
cg26752884 11 JRKL;CCDC82 96123217 0.002 4e-07 0.1994 65
cg04992638 17 LOC100133991;C17orf46 43339328 0.002 4e-07 0.2091 65
cg05795554 16 FANCA 89883212 0.004 8e-07 0.3764 65
cg25365565 6 HIST1H2BJ;HIST1H2AG 27101050 0.001 1e-06 0.4956 65

Studentized Residual QQ plots top 6 sites - raw PHQchange

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63127 
   65 

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63130 
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63127 
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63127 
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50136 
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63127 
   65

Leverage Plots top 6 sites - raw PHQchange

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Cook's Distance - raw PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ Baseline Methylation

QQplot of pvals based on INV PHQchange and CI

QQplot of filtered vs not filtered.

QQplot of filtered with CI

QQplot of filtered: with vs without Sex

Results based on INV PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg07219643 12 WSB2 118499016 0.004 1.0e-07 0.0564 65
cg23679073 2 ZC3H15 187350909 0.008 1.0e-07 0.0636 65
cg15286044 10 CRTAC1 99789971 0.013 7.0e-07 0.3260 65
cg00220389 17 NA 80455521 0.006 7.0e-07 0.3450 65
cg07696033 11 ALX4 44326410 0.008 1.1e-06 0.5156 65
cg20696752 17 LSM12 42143797 0.004 1.5e-06 0.7433 65
cg14613271 2 SLC5A7 108602931 0.013 2.2e-06 1.0000 65
cg02592615 6 HIVEP1 12012261 0.010 2.5e-06 1.0000 65
cg07399094 6 NA 3163461 0.007 2.9e-06 1.0000 65
cg26752884 11 JRKL;CCDC82 96123217 0.006 3.0e-06 1.0000 65

Residual QQ plots top 6 sites - INV PHQchange

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63127 
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63127 
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63127 
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63127 
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[[5]]
63127 
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63127 
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Leverage Plots top 6 sites - INV PHQchange

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Cook's Distance - INV PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ INV Baseline Methylation

QQplot pvals : INV PHQchange ~ INV Base Methylation

Results based on INV PHQchange ~ INV Base Methylation
CpG Chr Genes Pos beta pval p.adj size
cg23679073 2 ZC3H15 187350909 0.182 1.0e-07 0.0482 65
cg21746851 3 PRRT3 9994105 -0.108 6.0e-07 0.3119 65
cg08099331 16 DEXI;CLEC16A 11037187 -0.150 8.0e-07 0.3697 65
cg26719995 2 EMILIN1;KHK 27309153 -0.079 1.4e-06 0.7008 65
cg22327690 17 TRIM37 57179774 -0.105 2.6e-06 1.0000 65
cg09984518 19 AKAP8L 15529851 0.239 3.8e-06 1.0000 65
cg17006519 13 HNRNPA1L2 53191650 -0.040 5.7e-06 1.0000 65
cg20883684 2 C1QL2 119917385 0.109 6.5e-06 1.0000 65
cg14020595 4 SPATA5 124234087 -0.114 6.7e-06 1.0000 65
cg19156280 3 NGLY1 25825111 0.131 7.6e-06 1.0000 65

Residual QQ plots top 6 sites

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63127 
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64007 
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63127 
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Leverage Plots top 6 sites

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Cook's Distance : INV PHQchange ~ INV Base Methylation

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PCA on top sites - Scree Plot

PCA on top sites - biplot